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Aplus-Student-Notes-Biology-Unit-4-Joanna-FINAL

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Genotype: The genetic constitution of a cell. Normally with reference to a specific
characteristic.
Phenotype: An observable characteristic in an organism. This results from the genotype. In
many cases environment also plays a role.
Allele: An alternative/variant form of a gene
Gene pool: The total sum of all the alleles in a population
Genetic diversity: Variation in alleles and is dependent on the gene pool
Allele frequency: The total number of one allele for a specific gene/total number of alleles
for that gene in the population
Variation: The difference in alleles. Due to mutations
Genetic equilibrium: Allele frequency remains the same across populations
●
Any change in allele frequency shows that the population is not in equilibrium and
that there are some factors at work causing a change in allele frequency -- population
is evolving
Karyotypes: A set of chromosomes ordered by number and size
●
●
Haploid number = n
Diploid number = 2n
Why is variation good?
●
Helps a species survive and adapt to environmental conditions
●
It allows the environment to choose the ‘fittest’ alleles to survive
●
Species with little variation are at high risk of extinction when undergoing selection
pressures as there is a greater likelihood of individuals with selective advantage
being present with greater genetic/phenotypic variation. These species may also
suffer effects similar to inbreeding
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Genetic mutation: A random and unpredictable change in the sequence of nucleotides that
make up DNA
Mutagen: Any influence that increase the rate of mutation
A single change in the base sequence of the DNA or during transcription that disrupts triplet
code caused by substitution, addition or deletion
●
Missense mutation
○
●
Nonsense mutation
○
●
Amino acid sequence is ended early due to the mutation coding for a STOP
(substitution)
Silent mutation
○
●
One amino acid is affected → may change the functional shape of the protein
(substitution)
Causes no change to the amino acid sequence due to degeneracy of the
amino acid codes (substitution)
Frameshift mutation
○
Caused by addition or deletion of a base that alters the reading frame. All
codons/triplets are affected after the mutation
○
Protein will be non-functional
●
Affects sections of chromosomes.
●
Caused by nondisjunction during meiosis (not separating properly)
●
Block mutations caused by differences in one part of the chromosome:
○ Inversion
○ Duplication
■
One chromosome has a duplication of a part whereas the other
chromosome in the pair has none
○ Insertion
○ Deletion
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○ Translocation
■
One part of the chromosome breaks off and attaches to a different,
non-homologous chromosome.
■
Passed on to gametes
●
If all the genes are there still there, then the person is phenotypically normal.
●
Seen in the karyotypes
●
Aneuploidy: When an individual has an abnormal number of chromosomes (extra,
missing or bits of a chromosomes) due to nondisjunction in meiosis.
○
Down syndrome
■
○
Trisomy 21
Turner’s syndrome
■
Missing an ‘X’ sex chromosome
○
Alters the expression of hundred of genes at the same time → affecting
phenotypes greatly
○
A way for plants to form new species
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Polyploidy: When an organism has more than the normal number of sets of
chromosomes
○
A way for plants to form new species
○
Tend to be larger in size
○
Decreases genetic diversity of original plant as they cannot successfully
interbreed and hence reduce gene pool
Increases variation, hence increases genetic diversity, if the mutation produces a
functional protein
○ New allele has been added to gene pool as protein is functional
Population: A group of interbreeding individuals of the same species in a given area.
Evolution: Changes that occur in the phenotypes of a population over many generations.
Species: A group of organisms that can interbreed/mate to produce viable, fertile offspring.
Viable: To be able to survive.
Fertile: Can produce offspring.
Inbreeding: When organisms that are closely related to each other mate and produce
offspring.
●
More likely to produce offspring with a genetic disease (disease causing alleles are
more likely to be expressed)
Polymorphism: The presence of genetic variation within a population.
Selective agent: The one who enforces the selection pressure eg. Bird, human.
Selection pressure: Something that favours some individuals over others eg. Predation,
hunting.
Temporal Isolation: Mating times are out of sync.
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The process of which random evolutionary changes are selected for by nature in a
consistent, orderly, non-random way and favourable alleles are inherited over many
generations
1. Variation exists in a population.
2. A selection pressure or agent acts on the phenotypes of the members of the
population so that some members are more likely to survive and reproduce
3. The alleles that correlate with the characteristics that give survival advantage are
therefore more likely to be passed onto offspring and increase in frequency over time
(many generations)
4. This means that overtime the population evolves to suit their environment
●
Reduces genetic variation in gene pool
*format used to answer questions*
Variation
●
Phenotypic variation present in the population eg. colour
Environment
●
The environment decides which variations/traits are desirable for survival
Selection
●
Selection is caused by selective pressure/agent. What determines what lives or dies?
○ Environment, predation, parasitism or population pressure and competition
Inherit
●
The favourable alleles are then inherited from the parents to the offspring
Generations
●
Favourable alleles are inherited over many generations. Frequency of alleles
increase/decrease.
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Organisms with traits that are seen as desirable are selected and bred with each
other in order to increase the chance of producing offspring with the desirable trait.
The offspring with the greatest extent of the desired trait are chosen and bred with
each other. This process continues reinforcing the prevalence of that trait.
●
Humans are acting as the selection pressure.
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Suits the breeder but often does not increase the animal’s ability to survive in the
wild.
●
Tends to decrease the genetic variation of the gene pool and hence less biodiversity.
●
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○
The extent of genetic variation within a species decreases due to the
formation of a new species (offspring) which cannot successfully interbreed
with ancestors
○
Leading to greater susceptibility of whole population to pathogens or changes
in environmental conditions
Mating is not random
○
Females choose to mate with the most glamorous male
○
Males fight to reproduce
○
Asexual reproduction does not create new combinations of alleles and
hence does not produce new phenotypes on which selection can act.
How many times an organism reproduces matters more than long life span. As a
result, more alleles are passed on.
The movement of alleles between populations via interbreeding.
●
Migration: the movement of an organism into a new population
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Immigration: individuals entering a population and can increase diversity
●
Emigration: individuals leaving a population and can decrease diversity
●
In plants, this occurs through dispersal of seeds, spores or pollen
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Affects gene pool
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Change in genetic variation between one generation and the next due to chance events
●
More evident in small populations
The size of a population is severely reduced and the few survivors, by chance, are
unrepresentative of the original population as alleles may be lost. It is a selection pressure.
●
●
●
●
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eg. by famine, flood, disease etc
Genetic diversity is limited
Even if the species recovers (in numbers) there is less genetic variation
Less likelihood of organism with a selective advantage.
Population is at risk of extinction when a new selection pressure is present
A random process whereby a small group of organisms leave the original population and
forms a new separate population but the new population is not representative of the old
population.
●
●
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Low genetic variation
Can explain why some specific populations of people have higher incidences of
certain genetic conditions
eg. New settlement
One group of a certain species is separated from the original population due to a
geographical barrier which prevents gene flow (reproductively isolated).
Variation
●
Phenotypic variation present in the population eg. colour
Isolation
●
Isolation is caused by a geographical barrier prevents gene flow between the two
groups
Selection pressures
●
Separate environments mean that they experience different selection pressures
Changes in Alleles
●
The favourable alleles in each environment will be inherited from parents to the
offspring, causing change in allele frequency
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Mating
●
If the separated groups were brought back together they would be unable to produce
viable, fertile offspring due to isolation mechanisms
New species
●
They are then considered two different species
Evolution of a new species can be more rapid if only a small population is isolation by the
barrier. The effects of natural selection, founder effect and genetic drift can lead to rapid
speciation. Polyploidy and aneuploidy also.
Increases genetic diversity between the isolated groups
●
Members of the isolated groups can only interbreed with others in the same
population.
●
Each rat population is subjected to different selection pressures and therefor genetic
changes accumulate in the two populations, increasing the degree of diversity
between them.
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First eukaryotes ~ 1500 million years ago
Vertebrates ~ 500 million years ago
Mammals ~ 250 million years ago
Flowering plants ~ 200 million years ago
First hominids ~ 6 million years ago
The appearance of multicellular animals in the fossil record can be related to build up of
oxygen in the atmosphere derived from photosynthetic cyanobacteria. Flowering plants
(angiosperms), birds, and mammals rapidly radiated into niches left vacant by the extinction
of the dinosaurs.
Biodiversity: The variety and abundance of different species on Earth.
The law of superposition: The oldest strata (layers) of rock are at the bottom and the
youngest are at the top (except in cases of major movement).
Stratigraphy: Estimating the relative age of a rock strata by the position of layers using
igneous strata as a reference.
Biogeography: The study of the geographic distribution of organisms.
Half-life: Time taken for the amount of radioactive isotope to decrease to half its amount.
Preserved remains, impression or trace of an organism found usually in sediments,
hardened as rocks. They are evidence of life and evolution.
The fossil record shows:
●
That life in the past seems to have been relatively simple
●
Many species that used to exist are now extinct
●
Many extant (surviving) species don’t seem to have existed in the past
●
The fossil record shows the changes that have occurred in the types of organisms
living over time.
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1. Rapid covering in sediment (silt, sand, or volcanic ash with some moisture)
2. Protection from the elements and scavengers
3. Slow rate of decomposition (death in low oxygen, alkaline or cold environment so that
bacteria that normally decompose dead tissue cannot survive)
4. Further burial (further layers of sediment)
5. Little disturbance of site
Hard body parts make fossilisation easier to happen
●
Mineralised fossil (petrified fossil)
○ Minerals from the surrounding sediment leech into the bone and replace the
bone itself
○ Bone turns into rock (mineralised fossil)
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Mould
○ The organism decomposes slowly, leaving a cavity in the rock
○ When some of the rock erodes, an impression of the bone is left
●
Cast
○ Formed from a mould that was filled up by sediment (usually volcanic rock)
○ When the mould erodes away, the 3D shape of the organism is left
●
Trace
○ Footprints, teeth or claw marks, nests, eggs, tunnels (burrows), human tools.
•
Preserved
●
○
The actual organism is basically unaltered and stays intact. E.g. mammoths
that have been found in ice and frozen ground, insects preserved in resin
(tree sap).
○
The soft body parts are preserved as well as the hard parts.
Mummification
○
When organisms die in dry places like deserts/caves, they dry up so fast that
there is not enough time for even their soft parts to decay.
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Relative dating: The age of the rock/fossil expressed in relation to other
fossils/rocks (less specific).
○
Used to create eras/period.
○
Stratigraphy of rock layers.
■
■
■
○
Lowest sedimentary rock layer is the oldest (first to form)
Upper sedimentary rock layers are the youngest (formed later)
Disadvantage is that layer may be eroded, moved or reburied
Indicator/index fossils: Used to identify the relative age (which period of
time) of the rock strata they are found in
■
Must be:
●
●
Distinctive
Abundant
○
●
●
●
High variation within population to be able to adapt to
different environments/niches
Wide geographic distribution
Short time in geological history
○
Nearby volcanic rock is useful to date sediment as they are newly formed
rocks
○
Relies on the presence of index fossils
Absolute dating: The age of the rock or fossil expressed in years (more specific) by
using radioisotopes that decay at a given rate and measuring the ratio.
●
Carbon dating: The half-life of Carbon 14 is used to compare the ratio of
Carbon 14 to Carbon 12 in organic material to calculate absolute age
○
Carbon 14 is a radioactive isotope that decays to the stable product
Nitrogen 14
○
Half life of 5730 years
○
Can only be used to date organic compounds aged <50,000 years (no
carbon 14 left)
○
Age is determined by comparing the ratio of C14 to the initial C14 in
the actual fossil
■
■
■
All living things have the same percentage of carbon 14
When the organism dies, it stops cycling carbon 14
As the organism decays, the carbon 14 decays
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○
Benefits:
■
■
●
Used as living things are carbon based lifeforms
More accurate if organic compound is aged <50,000 years
Radiometric dating: The half-life of radioisotopes are determined and is
used to compare the ratio of the parent to daughter isotopes in igneous rocks
(inorganic) to calculate absolute age
○
Potassium/argon dating
■
Potassium 40 decays into argon 40
■
Half life of 1.25 billion years
■
The ratio of potassium 40 to argon 40 in the rock surrounding
the fossil is measured to determine the age
■
Used to date the surrounding rock as it cannot be used to date
a fossil directly as these elements are not usually found in
organisms
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Transitional Fossils
○ Fossils that are intermediate between forms (e.g. Archaeopteryx –features of
birds and reptiles)
●
●
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Homologous Structures
○
Features in different species that have a similar structure but a different
function
○
Evidence of sharing common ancestry
○
Divergent evolution
Analogous Structures
○
Structures that have the same function in different species but that may have
a different structure.
○
Evidence of similar environmental conditions/selection pressures.
○
Convergent evolution
Vestigial Structures
○
Reduced structure with no apparent function which may have had a function
in ancestors
○
Can be used as evidence of related organisms having diverged from a
common ancestor as they are remanments left by a recent common ancestor
Comparison of the form, structure and development of the early stages of embryos of
different vertebrate organisms to determine common ancestor
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When closely related species become more dissimilar over time, usually in response to
different environmental conditions/selection pressures.
●
Evidence: Homologous Structures
○
Structures that have similarity in basic structure due to sharing a recent
common ancestor, even though they may have different functions
When natural selection may act on distantly related species to produce similar adaptations
that are not due to shared ancestry but reflect that the species are exposed to similar
selection pressures
●
Evidence: Analogous Structures
○
Structures that are not necessarily similar in structure but carry out similar
functions due to similar selection pressures
Adaptive radiation is the rapid evolutionary diversification of a single ancestral species into a
number of specialised descendent species in order to take advantage of a variety of
ecological niches.
When all members of a species permanently dies out
●
Generally occur when the species is unable to adapt to a new selection pressure
●
When variation within a species is insufficient for some individuals to be favoured by
a selection pressure
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Absence of evidence of existence, such as scats or tracks.
A period of time during which an abnormally high number of species died out in a short time
span usually due to the involvement of major/global climate change (temperature changes,
meteorites, sea level, UV light)
●
●
Allows surviving species to expand and diverge → greater genetic diversity
○
○
Mass extinction resulted in many unoccupied niches
Natural selection enables different populations to specialise in different
niches, resulting in adaptive radiation
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Determining the precise order of nucleotides in a segment of DNA from equivalent
genes in different species to then be compared to determine relatedness
●
The more differences in the DNA sequence the less related the two species are
because there has been more time for them to accumulate different
mutation/differences
●
PCR
●
Better to compare DNA sequences than amino acid sequences because
substitutional point mutations might not alter the amino acid sequence (e.g. silent
mutation occurs as one amino acid can be coded for by more than one codon). There
is also more nucleotides to compare than amino acids (three nucleotides are required
to code for one amino acid). Much more accurate to look at DNA sequences.
●
Process of determining relatedness between two species using samples of DNA
○
A sample of DNA from each species is heated to 87 degrees so that they
become single stranded (dissociate)
○
The samples are mixed and cooled to 55 degrees so they will anneal (the
more similar DNA strands from each species, the more they will anneal with
each other)
○
The samples are once again heated to separate them to determine the Tm
(melting temperature)
○
Single stranded DNA absorbs ultraviolet light, which can help indicate what
temperature the DNA hybrid separates
○
Each degree measures the degree of change (only under 87%)
■
○
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Eg. 77 degrees mean 10% difference between the two DNA strands
High complementarity between the two sequences means higher Tm (melting
temperature) is needed to separate the hydrogen bonds. A high Tm means a
higher degree of pairing, hence the more closely related the species
DNA hybridisation compares the complementarity of nitrogenous bases within two
single strands of DNA from two different species by measuring the melting
temperature of the hybridised double helix formed by the two single strands. The
melting temperature indicates the complementarity and therefore relatedness
between the two species as the more hydrogen bonds formed requires a higher the
melting temperature.
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Small circular DNA found in mitochondria (different from nuclear DNA)
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Non-coding region as coding region is needed for aerobic respiration
●
Mutations occur at a higher and known rate (allows scientists to put a molecular time
clock on how long has passed since divergence from another species), therefore
mutations can be measured (how many genetic differences there are) which can
show how closely related two species are → molecular clock
●
The more differences in DNA, the longer the time since divergence/the less related
the two species are
●
Is helpful in determining relatedness as it is only passed down the maternal line (no
recombination) and has very few mutations so can be used to trace back numerous
generations.
○
Therefore variation between organisms is due to mutation only, not crossing
over and recombination or independent assortment
●
Cytochrome C is common between all species
●
Mitochondrial Eve
●
Shows more variation in African population
○
More resistance to disease
○
Other populations are founder effects due to migration→ reduction in genetic
variation
●
Equivalent proteins in different species can be compared to determine relatedness as
species that are more closely related are expected to have fewer differences in
amino acids of their corresponding proteins than species that are more distantly
related
●
Differences are due to mutations in DNA
●
Changes in the amino acid sequence appear more slowly than in DNA sequences as
some mutations may be silent, therefore is not as accurate as other methods
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Phylogenetic trees
○ Shows information such as:
■
■
When speciation occurs (split in the tree)
When two organisms shared a common ancestor
○ To see how closely related two species are, you need to look at how far back
in time their common ancestor is
●
■
If two organisms are closely related they diverged later (less time
available for individual mutations to accumulate in each of the species
as they shared a more recent common ancestor)
■
If two organisms are distantly related they diverged earlier (more time
available for individual mutations to accumulate in each of the species
as they shared a less recent common ancestor)
BMP4 (Bone Morphogenetic Protein 4) produced by most species, is coded for by a
master gene (regulatory gene)
○
Master gene
■
Controls other regulatory genes which control other structural genes
●
■
○
Cascade of events
Produce a range of phenotypes
The gene for Bmp4 is highly conserved throughout the animal kingdom
(across species and generations)
■
Highly conserved (does not mutate) → genes needed for basic
function
●
■
Means that we need it
That mutations occur in the genes coding for regulatory proteins that
control its expression NOT in the BMP4 gene itself
○
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○ Same genes turning on and off determine the shape of beak/jaw → matches
food source in their niche (arises from speciation and natural selection.
Expression of Bmp4 is selected for in different niches)
■
Timing and intensity (variation in expression)
■
Gene produces regulatory proteins (transcription factors) that control
other genes
■
Bmp4 protein is not a structural protein
○
Involves signal transduction
○
Bmp4 levels do not change in a single organism → variation is due to
variation in the population
●
More Bmp4 produces more deep and broad beaks in birds
●
Galapagos finches and cichlid fishes of Malawi are examples of adaptive radiation
and the differences in the beaks/jaw are due to the variation in expression of BMP4
which is dependent on the different feeding techniques/behaviours (due to the
different habitats)
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Dexterous hands and feet with five digits that can grasp or curl, with opposable
thumb in some cases
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Flattened nails on digits that are sensitive to touch
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Stereoscopic (3D) colour vision
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No tail
●
Locomotion is by brachiation (arm swinging), knuckle walking or bipedalism
●
Posture is partially or fully erect allowing hands to manipulate food, care for young or
use tools
A smaller subgroup of the hominoids consisting of great apes and humans, but not gibbons
(family hominidae).
●
Bipedal
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Very fine hair
●
Position of foramen magnum is centred under the skull
●
Larger brain compared to apes; well developed cerebral cortex
●
Smaller, rounder (parabolic) jaws and teeth
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Longer curved lower spine
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Bowl-shaped pelvis
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Less prominent brow ridge
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Shortened and less protruding faces
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Longer legs relative to arms
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Alignment with big toe with other toes
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Angle between the femur and tibia (leg bones) → better centre of gravity when
walking/supports weight on one leg
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Change in physical features over time
Skull
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Large brain compared to apes (large cranial capacity)
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Less protruded, thinner, smaller and more parabolic jaw and smaller teeth (reduction
of size of front teeth, especially canines)
○ Due to diet
●
Position of foramen magnum (large opening in the base of the skull through which
the spinal cord exits)
○ Towards back of skull, indicates walking stooped on all fours
○ Towards middle of skull, indicates walking upright
○ Affects the shape of spine
●
Reduced brow ridge
●
Reduced zygomatic arch
○ Due to diet
●
Forehead slopes less
●
Flatter face
Lower body
●
Bowl shaped pelvis and shorter hip bone: entirely support upright walking
○
●
Slant of femur and tibia allows upright walking so knee joint is directly below the
pelvis (adaptation for walking upright)
○
●
Larger cranial capacity
Presence of a heel: bipedal
○
●
Body weight can be supported on one leg as the other leg walks forward due
to appropriate centre of gravity
Increased space in the pelvis of which a baby would pass through
○
●
Wider pelvic outlet allows for offspring with a larger head and hence the
evolution of larger brain size which can correspond to increasing intelligence
that characterizes homo sapiens
Makse bipedalism more efficient and does a better job of supporting the
increased weight associated with bipedalism
Alignment of big toe with the rest of the foot: bipedal
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Spine
●
●
S shape suggests upright posture → bipedal
C shape suggests bent over posture → quadrupedal
Arm to leg ratio
●
Shorter arm to leg length ratio shows bipedalism as arms do not need to reach the
ground for knuckle-walking
Change in abilities over time.
Advantages of being bipedal
Must be a selective advantage
●
Stand taller
○
●
Able to scan their environment for potential predators or potential food/water
sources
Bipedal position is more efficient in keeping the body cool during activity in hot dry
daylight hours in open habitats in the tropics
○
Thermoregulation
■
●
Sweat
Frees the hands for manipulation and carrying objects while moving
○ Enabled the evolution of the precision grip
●
Could migrate over greater distances
Change in thinking over time.
●
Neural interactions became more complex as hands are free to use as a result of
bipedalism
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Cultural evolution
●
Cultural evolution refers to changes in human societies over time where those
changes are socially transmitted and passed down generations, not genetically
inherited and passed down generations.
●
Learned behaviours that are transmitted socially and passed down generations
●
○
Quick – learning not dependent on inheritance (can occur within one
generation whereas structural evolution occurs over many generations)
○
Traits can be transmitted by many unrelated persons
○
Transmission within or between generations
○
Acquired traits transmitted by teaching or imitation
○
Choice to accept or reject cultural traits
○
Transmission by written word, speech or vision/sign language
○
Change can be conscious and deliberate
Usually highly dependent on spoken or written language
○ Able to be passed on because we are able to speak/write
■
●
Storytelling and art
Facilitated by/involved with biological change (evolves independently of biological
change)
○
○
Bigger brain
■
Gained cognitive capacity (problem solving skills, cultural behaviours,
speaking and to pass knowledge on)
■
Ability for beliefs, language, symbols and ceremonies shared
symbolically by individuals
Development and use of tools may have been passed on through
generations, therefore requiring less use of sharp teeth for fighting. This may
have contributed to kaws with less sharp canine teeth.
Examples
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Development of nomadic hunter-gatherer societies
○
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Development of agricultural societies
○
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Knowledge about food, environment, seasons and social traditions
Frees the society to develop arts, writing, music, crafts, mathematics etc
Development of technological societies
○
Greater urbanisation, specialisation of roles in society and rapid technological
change
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Technological evolution
The ability to pass on knowledge on how to do things. The application of science by humans
to gain better control of the material environment (tools, machines, robots, medical
procedures)
●
Facilitated by biological change (evolves independently of biological change)
○ Bipedal locomotion
■
Freed hands for manipulation of objects
■
Tool making and technologies that increase human control over their
environment → more efficient hunting methods that provided a more
protein rich diet which lead to increased brain size or more efficient
hunting methods so that canines were not needed in order to kill prey
Why is the fossil record of hominins poor?
●
Fossilisation is an extremely rare event
●
Hominins don’t live in places conducive to fossilisation
●
Hominins have behaviours that make fossilisation unlikely
●
Hominins have no been around very long
Why are the fossils we have incomplete?
●
Complete fossil of an incomplete specimen
○ Exposure to scavengers, weather (erosion) before fossilisation
●
Incomplete fossil of a complete specimen
○ Disturbed rock layers (damage to the fossil) after fossilisation
Australopithecus africanus
●
Thought to be the extinct ancestor of the Homo genus
●
Most hominin fossils found are classified as Australopithecus → early hominin (more
ape-like)
●
Taung child (fossilised skull of a young Australopithecus africanus individual)
○ Discovered in 1924 in South Africa
●
Lucy from “Afarensis”
●
Used stones as tools (not shaped)
●
Limb proportions more human like
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Homo habilis (handy man)
●
First species to use stone tools
●
Fossils aged to approximately 2.5 million years old
●
Eastern Africa
●
Limb proportions more ape like
Homo erectus (upright man)
●
Fossils aged between 1.6 million years ago - 300,000 years old
●
Oldest hominin fossils to be discovered outside Africa (first hominin to migrate out of
Africa)
●
First evidence of controlled use of fire, clothing, living in huts/caves → increased
cognitive ability
●
Hunted systematically and used more complex, sharp tools
●
No speech yet
●
Common ancestor of neanderthalensis and sapiens
Homo denisovans
●
Fossils aged between 300,000 and 40,000 years old
●
Diverged from modern humans about 500,000 years ago
○ Diverged from a common ancestor of Homo erectus
●
Very closely related to Neanderthals, diverging from them around 300,000 years ago
●
Existed at same time as homo sapiens and neanderthalensis
○ Interbred with neanderthalensis in a different area
●
Based solely on DNA comparisons
Homo neanderthalensis
●
Fossils aged between 150,000 and 35,000 years old
●
Co-existed with Homo sapiens
○
Therefore not ancestors of modern humans
○
Probably competed for same food and resources as Homo Sapiens and
eventually led to their extinction (not as well suited to survive or compete with
Homo Sapiens)
○
Evidence of homo sapiens and neanderthalensis interbreeding in Asia and
Europe
■
mtDNA evidence
■
1-4% has been found in modern human populations
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●
Made advanced tools and clothing
●
Use of cave paintings
●
Large body and brain case with heavy brow ridges
●
Burial of the dead
Homo floresiensis (the hobbit)
●
Found in Indonesia, dated to approximately 38,000 - 18,000 years ago
○ Rainforest habitat
■
●
Large SA:V ratio, increased heat loss in hot environment, therefore a
selective advantage to be shorter.
A very short adult female with a small brain, which lived about 38 000 to 18 000
years ago. It appears they lived alongside Homo sapiens but could not compete with
the Homo sapiens.
○ Evidence for the parallel evolution (regional continuity) hypothesis
Homo sapiens (modern humans - ‘wise man’)
●
Appeared in Eastern Africa about 100,000 years ago
○
Out of Africa hypothesis: Hominins only existed and evolved in Africa until
100,000 years ago. Homo sapiens then migrated out across the globe
■
More variation in mtDNA of Homo sapiens in Africa compared to other
areas
■
More variation suggest a longer evolutionary history, therefore
supporting this theory
■
Populations outside Africa due to founder effects from migration which
causes populations to not be representative of the original population.
As a result. these populations have less genetic variation
○ Multi-regional hypothesis: Homo Sapiens evolved in multiple regions around
the world at the same time from Homo Erectus
●
■
Homo Erectus (1.5 mya ~ 0.3 mya) left Africa, then Homo sapiens
evolved in other regions from this ancestor.
■
Other homo fossils like homo floresiensis found outside of Africa
(transitional form?)
Out competed other human species and are now found all over the world
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●
Larger brain and slender build compared to most other human species
○ Complex cognitive abilities and resulting complex cultural practices/evolution
○ Thin skull
●
Forehead, chin, flat face, small teeth
If 2 or more species coexisted in a given time period:
●
They may have lived in different regions
●
They may not have competed for the same food
●
They may have competed for same food and resources, but this eventually led to the
extinction of one species (e.g. Homo neanderthalensis and Homo sapiens)
ENDONUCLEASES (restriction enzymes)
●
To produce complementary ends (sticky)
●
Cleaving DNA at a specific restriction site at a 6th base palindrome → read the same
on both strands
○ Different for different restriction enzymes
○ Cuts:
■
Cut in half (blunt ends)
●
■
Both strands are equal in length with no overhanging
nucleotides
Cuts up to the 5th base in both strands (sticky ends)
●
Overhanging nucleotides
●
Easier to join back together due to as the complementary
cohesive ends of DNA can anneal together via hydrogen
bonding.
■
Cannot cut within the desired gene
■
Same restriction enzyme should be used to cut as it will produce
complementary ends
■
Will cut in a 5’ to 3’ direction
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●
Naturally occurring in bacteria
○
Found naturally in bacteria where they provide a defence mechanism against
invading viruses (Bacteriophage)
■
○
Restriction enzymes can cut and destroy viral DNA before they can be
incorporated into the bacterial cell’s genome.
Cannot cut its own DNA as everywhere there is a recognition site for the
restriction enzyme, that recognition site with
ll be methylated, preventing the
restriction enzymes from cutting at that point.
■
Virus will be unmethylated and therefore will be cut
●
DNA ligase catalyses the joining of double stranded DNA fragments at their sugarphosphate backbones
●
Can only join pieces of DNA if they have complementary ‘sticky ends’ as these are
easier and more likely to ligate → must be cut with the same restriction enzyme
●
Blunt ends do not ligate as efficiently as sticky ends
●
Enzymes used to synthesise new strands (the strand is not completed) of nucleic
acid made of DNA nucleotides.
●
Taq DNA Polymerase (from thermus aquaticus bacteria can withstand high heat)
* Reverse transcriptase is used to copy mRNA into DNA so that the DNA
can be amplified by PCR or inserted into plasmids.
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To amplify target DNA → so that there is enough to be visible in the gel electrophoresis
●
DNA which acts as a template
●
Taq DNA Polymerase
○
Extends DNA
○
Resistant to high temperatures as it is from a thermoresistant bacteria.
As it is heat resistant, it does not denature at high temperatures during
PCR
●
DNA nucleotides
●
Primers
●
●
●
●
○
A short complementary sequence of a single stranded DNA to target the
DNA sample and specify the start and finish points for DNA replication
by flanking the target DNA
○
Two are needed as the nucleotide sequence is different at the start and
finish of the section of DNA that must be copied
○
Goes primer to primer after cycle 2
Coenzymes (magnesium chloride for Taq polymerase)
Buffer
PCR tube
Thermal cycler
All placed in a plastic tube in DNA thermocycler
1. Denaturation
○
DNA is heated to 95℃ to denature the double stranded DNA molecule into
single strands by breaking hydrogen bonds between complementary base
pairs
2. Annealing
○
Mixture is cooled to 55℃. Specific and complementary primers bind to
flanking regions of the target DNA sequence.
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3. Extension
○
DNA is heated to 72℃ degrees so Taq DNA polymerase can extend the
primer by adding complementary nucleotides to the template DNA strand at
its optimal temperature
●
Three stages of the cycle is repeated for about 35 – 45 cycles
●
Copies of DNA increase by 2^n, where n is the number of cycles
●
Primers are added because DNA polymerase cannot bind to a single strand
●
Process is extremely sensitive (any contamination in original sample will be copied
over and over again)
●
Technique used to separate out fragments of DNA based on their:
○ Size
■
Smaller fragments travel further and faster than larger fragments
through the porous gel as they move through the pores with less
resistance. Hence, shorter fragments travel the furthest distance in
any given time compared to longer DNA fragments
○ Charge
■
DNA has an overall negative charge due to phosphate groups in its
backbone and therefore migrates towards positive electrode and is
repelled by the negative electrode
●
DNA is loaded into a well at the top of the gel (negative electrode end) and travel to
the positive end as DNA is negatively charged as an electrical current runs through
the gel
●
Gel is made of agarose, which has tiny pores allowing DNA fragments to move
through the gel
●
Molecular weight ladder control/standard DNA fragments of known lengths
○
Contains bands (fragments) of DNA of known lengths
○
Acts as a standard of comparison to determine the size/length of unknown
fragments of DNA (in base pairs)
○
Conditions of every gel are different, so need a standard to show how DNA
fragments will run under different conditions.
■
Temperature and pH of buffer solution
■
There may be slight variations in how the standard separates on
different gels.
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●
Negative control
○ PCR mixture except the DNA to make sure sample is not contaminated
■
●
No band
Gel is then stained with ethidium bromide
○ Ethidium bromide diffuses into the gel and sticks onto the DNA
○ Fluoresces pink to show DNA
●
Used to make genetic fingerprints unique to an individual
○
●
DNA of individuals is different, therefore will be cut at different places and
produce fragments of different length.
To carry foreign DNA and insert it into bacteria to transform it by incorporating it into
the bacteria’s genome and therefore transcribe and translate the desired gene
Plasmids are found in the cytosol of bacteria → naturally move between bacteria and can be
inserted into the bacterial chromosome and be transcribed and translated.
●
This refers to inserting a gene of interest into a bacterial plasmid (vector)
●
Process:
a. Cut the gene of interest using restriction enzyme (Look for a 6th base
palindrome upstream and downstream of the gene for restriction enzymes to
cut the gene out) → MUST NOT CUT WITHIN THE DESIRED GENE
b. Cut the bacterial plasmid with the same restriction enzyme so that you
have complementary sticky ends
c. Mix the two together and add DNA ligase
d. The DNA ligase will help bind the complementary sticky ends of the gene of
interest and the plasmid together (between an antibiotic resistance gene)
e. Now called a recombinant plasmid as it has taken up gene of interest.
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●
This refers to bacteria taking up a plasmid
●
Process:
a. Mix bacteria with plasmids
b. Heat shock at 42℃ for 45 seconds
c. This prepares bacterial cells by opening up pores in the cell membrane
allowing plasmids to move into bacterial cell
d. Plasmids are not naturally attracted to bacteria, so to make them more
attractive, a salt solution could be added so that the positive ions help attract
the negatively charged DNA of the plasmid to be attracted into the bacterial
cell
●
Approximately one out of every million bacterial cells takes up a single copy of the
plasmid
●
Plasmid used has two antibiotic resistance genes, therefore the bacteria containing
the plasmid can be identified by adding antibiotics to the culture (agar plate)
a. The transgenic bacteria can be identified → antibiotic acts as selective agent
■
Because only transformed bacteria containing the plasmids carry the
antibiotic resistance gene therefore will be able to grow whereas the
bacterial cells not containing the plasmid will not grow
■
Bacteria that are resistant to one antibiotic but not the other are
recombinant due to the gene of interest splitting the antibiotic
resistance gene in half when it joins
●
Use to produce proteins in mass amounts
●
Can be taken up by a plant cell to transcribe and translate the DNA to form new
strain
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Legal: Concerning the protection that laws and regulations provide
Ethical: Concerning what is moral or right
Social: Concerning how society and individuals will be affected
●
The production of many identical copies of a gene allowing scientists to make large
amounts of a protein
●
Involves recombinant plasmids
See ‘Making a Recombinant Plasmid’ and ‘Bacterial Transformation’
Advantages:
●
●
●
Reduced costs of therapeutics made with bacteria
Wider access to treatments
Employment opportunities in the biotechnology industry
Disadvantages:
●
Misuse for non-therapeutic purposes (performance enhancing drugs)
Advantages:
●
●
Human recombinant proteins more effective than proteins purified from other animals
New and safer vaccines possible
Disadvantages:
●
Risk of contamination by bacterial molecules
Advantages:
●
Use of bacteria addresses philosophical, cultural or religious objections to animal use
Disadvantages:
●
Manipulation or shifting of genes may be seen as unethical, regardless of purpose
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●
Producing a unique genetic profile of an individual using non-coding nuclear DNA
(STRs)
●
Done to compare two people
○ Forensics
○ Paternity cases
●
●
●
Helps to develop a DNA database
Identify victims in mass disasters
Involves PCR and gel electrophoresis to match STRs
●
Short Tandem Repeats
○
Little pieces of DNA that everyone has (repeats of the same small sequence
of bases)
○
Found in the non-coding region and is highly mutable (in length) and therefore
hyper variable between people
■
Substitution mutations have no effect on length
Advantages:
●
Creation of a DNA samples data bank
Disadvantages:
●
Privacy → DNA samples cannot be obtained from a person unless they give their
permission
●
Can be ordered to give DNA sample if strong evidence they committed a crime (but
later destroyed if found not guilty)
●
●
DNA is stored for up to 10 years in some countries
Creation of a DNA samples data bank
Disadvantages:
●
Contamination of samples taken from a crime scene or at lab
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Advantages:
●
●
Person’s ancestry can be determined easily
Solving crimes
●
To determine if a person carries a faulty gene, or develop a genetic disorder, that can
be passed onto offspring and can be done in two different ways:
○ Karyotyping
■
■
■
■
Sex
Aneuploidy
Translocation
Can be done with noninvasive prenatal testing (6 weeks pregnant)
○ The determination of the actual sequence of nucleotides in a DNA strand
■
■
DNA sequencing
PCR and gel electrophoresis
Disadvantages:
●
●
●
●
●
Informed consent for DNA sampling
Security of stored genetic data
Legal access to genetic information
Reliability of DNA as proof of guilt or innocence
Abortion
○ Child with disease
○ Child that has unwanted sex
Advantages:
●
Potential to correct mutations (gene editing)
Disadvantages:
●
●
●
●
Accuracy (possible false positive and false negatives)
Doesn’t show the severity
Intervention in evolution (altered inheritance)
Changes human gene pool
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Advantages:
●
Reproductive decisions
Disadvantages:
●
Privacy due to storing people’s genetic information
●
Discrimination (insurance companies refusing life/health insurance and employment
and finding a partner)
●
Cost
●
Psychological effects
○ Depression
●
Changing the gene pool
●
Abortion
○ Incomplete information about severity of disease
●
Baby’s consent
●
Preventative measures/treatment
●
Life insurance for the baby is compromised
●
Consent from parents
●
Provides parents and doctors with information
●
Privacy
●
Whether the data is secure
●
Changing the gene pool
○ Selective breeding
●
Wastage of embryos
●
What traits do we allow to be tested?
○ Selective breeding
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●
An organism that has had its genome artificially altered so they express the desired
characteristic
●
Can be both transgenic or antisense genetic engineering
○ Antisense
■
Artificial complementary strand inserted in an organism to stop the
translation process by binding to the mRNA before it binds to a
ribosome
●
Recombinant plasmids
●
An organism that has had genes from an unrelated species inserted into its genome
→ due to genetic code being universal
●
Almost any gene transferred from one organism to another will express the protein
that is expressed in the original organism.
●
●
●
It is a GMO
Allows for crop productivity
Recombinant plasmids
Advantages:
●
Increased food supply, nutritional content and food quality
○ Less competition for resources from other plants so a greater yield from crop
●
Expanded range for growth of agricultural species
●
Labelling and consumer choice
Disadvantages:
●
Access to the technology (social equality/inequality)
●
Patents and pricing (control of access by biotechnology companies)
●
Costs to farmers
●
Cross pollination between GM and non-GM crops → organic farmers who border
GMO farmers may experience this and therefore lose their certification as they
cannot guarantee that their crops are 100% organic
○ Loss of business/livelihood
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Advantages:
●
Genetic variation in agriculture
●
Doesn’t kill useful insects
●
Less chemicals release into environment as less insecticide/herbicide is used
●
Less use of antibiotics
Disadvantages:
●
Reduces gene pool and therefore diversity of specific plant/animal
●
Other organisms depend on the crop as a source of food. Therefore making the crop
lethal to insects disrupts the food web
●
Safety of consuming GMO’s
●
Cross pollination between GM and wild plants/animals
●
Cross pollination between GM and non-GM crops/animals
●
Viability of transgenic organisms in the wild
●
Health of GMO’s
Disadvantages:
●
Violation of animal rights
●
Human self-interest overrides ethical treatment of other organisms
●
Intervention in evolutionary processes
●
Ownership of crop by one corporation
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As world populations become larger and humans come into closer contact with other
animals, new diseases have emerged. Controlling these diseases requires a global effort
Organisations that monitor global disease work on:
●
●
●
Early detection
Containment
Early treatment
Endemic: When a disease is regularly present among a particular group of people or in a
particular area
Emerging disease: A disease that has not been seen before. May be caused by a mutation
of existing pathogens
Outbreaks: Suddenly appears in a restricted locale or population
Epidemics: Within a community, large increase in number of people affected by pathogen
●
Increase in virulence
○ Change in antigen/mode of infection due to mutation
●
New pathogen introduced into community
Pandemics: Disease crosses social, ethnic and national borders and causes an epidemic in
at least one other country.
Isolation: Separation of people who are already sick from the general population
Quarantine: Separation of healthy people or animals who are known to have been exposed
to a pathogen or infected individual
●
●
A new pathogen emerges to which there is little to no natural immunity in human
populations
○
Original strain mutates to form new strain
○
Genetic drift occurs gradually and this eventually changes the antigens of
pathogen
○
New antigen is not recognised by host’s immune system
Pathogen is easily spread (airborne) between individuals
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●
High volume of transport or movement of the pathogen.
○
With migration, there is the potential to introduce pathogens to a new area
(e.g. Influenza)
●
Difficulty in detecting, diagnosing or tracking the individuals who are initially infected
●
Lack of herd immunity
○
●
Human behaviour
○
●
Not enough people getting vaccinations/booster vaccinations → B memory
cells have a limited life span
Has an impact on the emergence and re-emergence of diseases, including
STI’s or HIV
Changes in farming practices and food production
○
Changed over centuries to adapt to an increasing population and
globalisation
○
There is a greater demand for meat, etc., meaning that more farming
practices exist and are closer to human populations. This allows diseases in
animals to transfer to human more easily
○
Populations have no previous resistance to these new diseases
●
Uncontrolled or inappropriate use of antibiotics that provides bacteria with an
opportunity to develop immunity against antibiotics
●
Lack of sanitation and poor hygiene
●
○
Outbreaks are more common in underdeveloped countries due to poor
infrastructure for reliable sanitation amenities
○
Existing pathogens can emerge in new locations and among populations that
lack the ability to recognise and deal with it early enough to prevent it
spreading
Control and Containment of Disease
○
○
○
○
○
○
○
Prevention
Isolation and quarantine
Control carriers
Eradication of vectors
Vaccination
Education
Response plans
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●
Analysing the structure/mechanisms of the pathogen and specifically designing,
artificially, a drug that blocks/mimics the action of the pathogen to interfere with the
pathogens life cycle, preventing the development of that particular disease
○ Must not have any adverse effects
○ Specifically bind to substance, rendering it unable to bind to substrate
○ Specifically bind to substrate, preventing binding to an enzyme
●
Better to target the virus than the target cell
○ The drug may affect the functioning of the healthy cell
■
Side effects from the blockage of cell receptors
●
Hormone receptors
●
Identifying the molecular cause of a disease/disorder/pathogen/antigen
●
Design of a medication (drug) which uses a complementary shape and charge of the
molecule to stop a reaction or binding to the active site/receptor
●
Does not affect any other system/body or no adverse reaction/side effects
●
Specific to a disease/disorder/antigen
●
For a drug to be effective against a number of strains, need to find a common
structure between them.
●
If the requirement is to increase the intracellular concentration of the substrate, then
either a competitive or non-competitive inhibitor will serve, since both will inhibit the
utilisation of substrate, so that it accumulates.
●
However, if the requirement is to decrease the intracellular concentration of the
product, then the inhibitor must be non-competitive. Increasing the concentration of
substrate does not affect a non-competitive inhibitor.
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●
Involves analysing the structure of a pathogen or disease-causing molecule (antigen)
and using this information to design a drug that mimics or blocks the action of the
disease-causing agent.
●
Used to kill pathogens on surfaces such as door handles and hospital equipment
●
●
Chemicals used externally on living tissue to kill pathogens
Can break down lipids/disrupt cell membranes and denature proteins
●
Used to treat bacterial infections
●
Naturally occurring molecules produced by fungi and bacteria which can then be
extracted and modified to improve their effectiveness.
●
Work by preventing the assembly of the bacterial cell wall hence removing the
bacterial ability to reproduce or to repair its DNA
○ Doesn’t kill bacteria, stops the bacteria from growing (stops binary fission)
○ Target the cells of bacteria, without damaging cells of the host organism
●
However, bacteria can mutate to become resistant to drugs
○
Bacteria may reduce intake of drug into the cell
○
Alter the target molecule to which drug attaches
○
Pump the drug out of the cell
○
Enzymatically deactivate the drug
○
Although scientists are working on developing new antibiotics, there is a
concern that a strain of bacteria will emerge that is resistant to all antibiotics
●
Drugs that suppress the action of histamine and used in treatment of allergies and
inflammation by binding to histamine receptors
●
Competitive inhibitor
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●
Inhibits the reproduction of viruses → interfere with the virus life cycle
●
Good targets include:
○ Capsid/envelope proteins
○ DNA/RNA polymerase enzymes coded for by viral genes
●
●
Modes of action:
○
Preventing virus from entering the cell by binding to receptors/antigens that
allow the virus to enter
○
Inhibiting enzymes that catalyse reproduction of virus genome
○
Blocking transcription and translation of viral proteins
○
Preventing viruses from leaving the cell and so preventing the infection of
other cells
○
Monoclonal antibodies
Drug Resistance
○ Resistance can also evolve to antiviral drugs, especially in patients with
compromised immune systems
●
Most effective if an antiviral agent was able to kill viruses without killing the host cell
●
Used to target fungal infections
●
Drug Resistance
○
Resistance to antifungal treatments is also an emerging problem. The yeast
Candida which causes skin infections and thrush is a serious problem when it
gets into the bloodstream. Resistance of Candida to antimycotics (drugs that
work against fungal infections) is a growing problem in hospitals and in
immunocompromised patients (such as those undergoing chemotherapy or
with HIV/AIDS).
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●
Developed at CSIRO in Australia and one of the first designed by this process
●
Relenza blocks the active site of neuraminidase (competitive inhibitors) →
neuraminidase triggers the virus release from the host cell by cutting the connection
between the other surface protein (haemagglutinin) and a host cell receptor molecule
○ Not effective long term
○ Virus will evolve to become immune to the Relenza
●
Relenza has complementary shape and charge to this surface protein and therefore
acts as a competitive inhibitor
●
Antigenic variation
○
●
●
●
●
Some pathogens are highly mutable and hence change their surface antigens
as they grow and reproduce
Immunity to digestive enzymes
Some bacterial spores are resistant to immune attack
Cysts
Attack on the immune system
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